W7L1 Tues human population genetic P3

Question 1

Sequencing ancient genome

Answer 1

-sequencing DNA from well dated fossil five us clear temporal boundaries for population processes
-also give us problem
-identify genetic contribution from population not described in fossil or archeological record
-identify unexpected relationships between group
-contradict finding made

Question 2

2010 two archaic hominid genome

Answer 2

-complete genome from Neanderthals and denisovian
-comparison of these genomes to modern day humans clearly showed admixture occurred between all these group

Question 3

Archaic hominid introgression

Answer 3

-human - Neanderthal : 1-2% introgression
-Human - denisovan 1-4%
-archaic introgression is geographically structured
-the more we look, the more we find

Question 4

Neanderthal introgression into our genome

Answer 4

-all individual of non-African descent alive today carry 1-2% Neanderthal DNA (not the same 1-2% in everyone)
-one main admixture pulse around 60-50KYA (single instance of viable maiting)
-Neanderthals covered most of Europe, and as Far East as Siberia
-Human-Neanderthal TMRCA 700-500KYA

Question 5

Benefit of introgression

Answer 5

Many immune loci are clear sign of adaptive introgression from both Denisovans and Neanderthals
-Other traits include fatty acid metabolism, skin pigmentation, high altitude adaptation
-Two Denisovan variant in TNFAIP3 are protective against some type of microbial infection and spread beyond PNG and Australia

Question 6

Cost of introgression

Answer 6

• Some regions of the human genome are consistently depleted of introgressed DNA
• In other regions, introgressed alleles have been associated with lupus,diabetes, metabolic syndrome…
• There is (and was!) strong selection against introgression genome-wide

Question 7

Complex geography of Denisovan introgression

Answer 7

• Denisovans have a very limited fossil record and remain relatively unknown
• Sister group to Neanderthals, TMRCA Denisovan-Neanderthal: ~400 KYA
• Admixture today is highest in Indigenous Peoples of Australia and Papua New Guinea (2-4%)
• Most East Asians carry 0.1-2%
• Port Moresby, PNG, is 9000 km from Denisova cave.

Question 8

Archaic hominin population dynamics

Answer 8

• PSMC analyses predict small population sizes for Denisovans and Neanderthals
• PSMC, broadly: find coalescent for each bit of the genome, ask how old it is in general
• This leads to reduced heterozygosity and increased genetic drift

Question 9

The peopling of Europe (old version)

Answer 9

• First colonized by anatomically (and, from their tools, culturally) modern humans ~45 KYA
• Survive the Ice Age (started 18KYA) in southern Europe; it’s too cold up north.
• ~10 KYA mingle with incoming farmers from the Near East, nice admixture cline.

Question 10

The peopling of Europe (current best version)

Answer 10

Present-day Europeans are the product of admixture between 3 ancestral groups
* Original settlers 45 KYA contribute nothing to the present
* Hunter Gatherers expand 19 KYA but Neolithic farmers outcompete them ~8 KYA.
* 5 KYA, one more migration from the Caucasus and the Eurasian steppe.
* In Europe, population replacement is the norm (Lazaridis et al, 2014)